You will notice that many have comparative tracks based on similarity to known proteins already generated. You can also pursue a similar methodology yourself to perform cross-species annotation. What you eventually will want to do is map any annotation hits to a reference database that will provide EC numbers.

Once you have gene bounds/regions identified as targets, genome conservation "multiple-alignments" (the output often call "MAF" format) are where you'll want to go next. Not all genomes have this pre-computed nor will be in genome clusters that suite your research. And this can be a slightly tedious process to go through. Still, review how MAFs are created at UCSC in these track's methods, Microbes (link above) or others at http://genome.ucsc.edu. This particular method is the gold standard as far as I am concerned for global genomic arrangement analysis.

When you review methods, in the above or other publications (my short-hard here this is how much discovery/annotation is done, more or less, but look at pubs in your field), many tools to perform these operations will be in the Tool Shed http://usegalaxy.org/toolshed, as will alternate tools to perform similar functions, for most any data you wish to generate. Others tools can be wrapped and added. Test and build a workflow. These are for use in a local/cloud Galaxy: http://wiki.galaxyproject.org/BigPicture/Choices

Others who are currently performing bacterial analysis such as this are welcome to post more info (please!), Jen, Galaxy team